search

maccallumlab / meld

Modeling with limited data
http://meldmd.org
Other
54 stars 28 forks source link

Make REST2 scale AMAP potential #44

Open jlmaccal opened 6 years ago

jlmaccal commented 6 years ago

The REST2 transformer should scale the AMAP potentials along with the dihedrals.

jlmaccal commented 6 years ago

This should be straightforward.

We need to:

cing commented 6 years ago

It's probably worth noting that the AMAP potentials packaged with MELD were only parameterized for use with implicit solvent. Specifically, ff12sb+gbneck2 (see: https://www.ncbi.nlm.nih.gov/pubmed/26574266). So, enabling support for REST2 with AMAP might not be a good idea in this specific case but there's no harm in supporting it. As a side note, even ff14sbside has never been properly validated with these AMAPs.

jlmaccal commented 6 years ago

Actually, this is a good point. We probably shouldn't even allow use_amap to be set with explicit solvent.

cing commented 6 years ago

Scaling CMAP for REST2 still seems like it should be supported in preparation for eventually having CHARMM with CHARMM CMAPs working (which were parameterized with explicit solvent).

jlmaccal commented 6 years ago

OK, let's do both then. I'll add a PR for the compatibility check.

alberto99 commented 6 years ago

The new generation of Amber post ff14 will also have cmaps for explicit solvent.

On Sun, Jul 15, 2018, 01:52 Justin MacCallum notifications@github.com wrote:

OK, let's do both then. I'll add a PR for the compatibility check.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maccallumlab/meld/issues/44#issuecomment-405069264, or mute the thread https://github.com/notifications/unsubscribe-auth/AAM1nOPOTSY8MSNnQvGzH6nfUWxP2tuyks5uGtisgaJpZM4VPtvF .

jlmaccal commented 6 years ago

The new generation of Amber post ff14 will also have cmaps for explicit solvent.

Right, but those will be added directly by Amber. So we'll have to scale them, but we won't have add them ourselves. This will probably required updating the Amber parser in OpenMM, as I don't think Amber currently supports CMAPs in Amber format files?